Genetic Analysis Program
The Genetic Analysis Program is a scientific research group focused on utilizing JGI generated sequence.
Sequence Variant Discovery
Much of our efforts are focused on identifying sequence variants that may contribute to observed trait differences within a given species through the use of resequencing and genotyping. For instance, studies are ongoing to identify sequence variants that explain trait differences such as disease resistance within poplar trees (Populus trichocarpa).
New Sequencing Technologies
Studies are under way to explore the biological applications of new sequencing technologies (such as 454 and Solexa) that are capable of generating large datasets of short DNA sequence reads. Our goal is to guide JGI user programs by providing state of the art examples of the utility of these cutting edge technologies.
Alignment of Illumina "short reads" for Populus trichocarpa resequencing project.
Varying colors within a column indicate single-nucleotide polymorphisms.
Comparative Analysis
Through the use of comparative sequence analysis, our group is identifying functional sequences in the genomes of chordates sequenced by the JGI, including human (Homo sapiens), frog (Xenopus tropicalis), amphioxus (Branchiostoma floridae), sea squirt (Ciona intestinalis) and pufferfish (Fugu rubripes). Through these efforts, we have catalogued a large number of evolutionarily conserved modules of which a significant fraction has been shown to act as transcriptional enhancers of gene expression. These findings have led to a systematic effort to catalogue gene enhancers through a transgenic mouse assay. The data can be found at http://enhancer.lbl.gov.
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